Visualizing transcript structure and annotation using ggplot2

A minimal desktop app for easy and convenient gene annotation and lookup.

Annotate DNA sequences for Gene Ontology terms

Deep learning methods for feature selection in gene expression autism data.

Pipeline for the identification of (coding) gene structures in draft genomes.

Structural variant VCF annotation, duplicate removal and comparison

An R framework for phylostratigraphy

fastest GTF/GFF-to-BED converter chilling around

GeneSCF moved to a dedicated GitHub page, https://github.com/genescf/GeneSCF

high-performance BED-to-GTF converter written in Rust

Find Prokaryotic DNA methylase genes in proteins, contigs, or genomes

MetaDome is aimed at professionals in the (bio-)medical field of human genetics who wish to visualize the position of their mutation of interest in the context of general population-based genetic variation and provide detailed information of pathogenic variants found across homologous domain positions.

cool BED-to-GFF3 converter that runs in parallel

The post-TOGA processing pipeline

scripts associated with yam genome assembly

Analysis workflow to generate fungal assemblies, generate gene structural and functional annotations

Integrative systems analysis identifying the associations between genes and biological process or modules.

GTF/GFF per gene non-overlapping exon length calculator

Co-occurrence of enzyme domains

Supplementary code for the paper: Incomplete annotation has a disproportionate impact on our understanding of Mendelian and complex neurogenetic disorders

Package to gather gene information, annotations, and functions

A new annotation file format based on JSON, containing all information stored in the GenBank format but with advantageoius parsing and information structure properties.

The related code of the master thesis, "Using deep learning to predict gene structures of the coding genes in DNA sequences of Arabidopsis thaliana"

long read differential expression analysis and splice variant analysis

ncRNA identification, annotation and functional prediction

A toolkit for identifying gene homologs in closely related species.

Genome Copilot: AI-Interactive Genomic Visualization + Variant Risk Screening

Stone Lab @ CSUEB Collaboration Projects focused on Plant Bioinformatics

Enables Gene Ontology (and other feature annotation) enrichment calculations and comparisons between feature sets.

This is a recipe to make my gene matrix